Gene expression is a complex process that encompasses the sequential transfer of a cell's genetic information from its DNA into mRNA molecules and then into functional proteins. Specific RNA surveillance mechanisms monitor this process and are responsible for degrading defective mRNAs to protect the cell from producing aberrant proteins. Nonsense-mediated mRNA decay (NMD) is a conserved RNA surveillance pathway that detects and destroys mRNAs encoding premature termination codons (PTCs), thus preventing the translation of truncated products. As an important modulator of disease pathology, the NMD pathway is the target of several therapeutic strategies currently in development. In addition to targeting aberrant mRNAs, NMD also regulates normal gene expression, often via regulated changes in alternative splicing. Furthermore, NMD is required for proper embryonic development in multiple organisms. Despite significant research, however, the role of this process in cellular homeostasis and the mechanisms that govern its activity remain incompletely understood. This proposal uses high-throughput sequencing combined with molecular biological and computational techniques to investigate the role of the NMD pathway in mouse embryonic stem cell (mESC) gene expression. Towards this goal, those mRNA isoforms whose stability and translational efficiency are regulated by NMD and the mRNA features that determine their susceptibility to this pathway will be determined. Messages that directly associate with Upf1, an essential component of the NMD pathway, will also be identified. The results of these studies will illuminate the breadth of the impact that this RNA surveillance pathway has over gene expression and the extent to which these effects extend beyond the clearing of aberrant mRNA molecules, questions particularly relevant to understanding the repercussions of NMD-suppression therapies. Furthermore, these studies will specifically address the role that the essential NMD factor, Upf1, has in mRNA expression in early development and may help to explain the reasons for the dependency of embryogenesis on the NMD pathway. !